Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005992.1 Hibiscus syriacus cultivar Beakdansim tig00014097_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 73904
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:366 original size:30 final size:31
Alignment explanation
Indices: 330--400 Score: 108
Period size: 31 Copynumber: 2.3 Consensus size: 31
320 ATTACCTGAT
*
330 ATATGTGATAAGAAGCCAT-AGTTTATATTC
1 ATATGTGATAAGAAGACATAAGTTTATATTC
360 ATATGTGATAAGAAGACATAAGTTTATATTC
1 ATATGTGATAAGAAGACATAAGTTTATATTC
* *
391 TTATATGATA
1 ATATGTGATA
401 TGATATGTGA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
30 18 0.49
31 19 0.51
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.38
Consensus pattern (31 bp):
ATATGTGATAAGAAGACATAAGTTTATATTC
Found at i:533 original size:21 final size:20
Alignment explanation
Indices: 500--538 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
490 TTCTACTTGT
500 TCCTTCGGACATATATGTAA
1 TCCTTCGGACATATATGTAA
*
520 TCCTTTGGAACATATATGT
1 TCCTTCGG-ACATATATGT
539 GGTACTTGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.38
Consensus pattern (20 bp):
TCCTTCGGACATATATGTAA
Found at i:5690 original size:62 final size:62
Alignment explanation
Indices: 5595--5741 Score: 174
Period size: 62 Copynumber: 2.4 Consensus size: 62
5585 CAGAGGAGCA
* *
5595 AATCATTGACTTCCTAGTGAAGATAAGTCAACCTTT-TCTATTCAGGACTCCCCAGTAGAGTC
1 AATCATTGACTTCCTAGTGAAGATAAGACAACCTTTGTC-ATTCAGGACTCCACAGTAGAGTC
* * * *
5657 AATCATTAACTTCCTCA-TGAAGATAA-ACGAACCTTTGTCATTCATGATTCTACAGTAGAGTC
1 AATCATTGACTTCCT-AGTGAAGATAAGAC-AACCTTTGTCATTCAGGACTCCACAGTAGAGTC
* *
5719 AATCCTTGACTTCCTTGTGAAGA
1 AATCATTGACTTCCTAGTGAAGA
5742 GAAATTAATT
Statistics
Matches: 72, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
61 1 0.01
62 68 0.94
63 3 0.04
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (62 bp):
AATCATTGACTTCCTAGTGAAGATAAGACAACCTTTGTCATTCAGGACTCCACAGTAGAGTC
Found at i:6050 original size:137 final size:136
Alignment explanation
Indices: 5795--6143 Score: 464
Period size: 137 Copynumber: 2.6 Consensus size: 136
5785 TAAATTATCA
* * ** *
5795 AAAAAGAAGATGGTCAGATGTCCTCATCACGATTGAACAATGTCATCCACCGTCCAGATCTCCTC
1 AAAAA-AACATGGTCAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGACCAGATCTCCTC
* * * * *
5860 ATCACATAGGAGCCGCGTCATCCTTATATAACCAAAATTCCTTATCGCATAGGAACCATGTTATC
65 ATCACGTAGGAGCCGCGCCATCCTTAGATAACCAAAATTCCTCATCGCATAGGAACCATGTT-TA
5925 TCCATTAT
129 TCCATTAT
* * ** * *
5933 AAAAAAATATGGTCAGACGTCCTCATCACGAAGGAACAGTGGAATCTACCGACTAGATCTCCTCA
1 AAAAAAACATGGTCAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGACCAGATCTCCTCA
* *
5998 TCACGTAGGAGTCGCGCCATCCTTAGATAACCAAAATTCCTCATCGCGTAGGAACCATGTTTATC
66 TCACGTAGGAGCCGCGCCATCCTTAGATAACCAAAATTCCTCATCGCATAGGAACCATGTTTATC
6063 CATTAT
131 CATTAT
* * * * **
6069 AAAAAAACATGGACATACATCCTCATCATGAAGGAACAATGTCATCCACTAACCAGATCTCCTCA
1 AAAAAAACATGGTCAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGACCAGATCTCCTCA
6134 TCACGTAGGA
66 TCACGTAGGA
6144 CCTACGTCAT
Statistics
Matches: 182, Mismatches: 29, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
136 72 0.40
137 105 0.58
138 5 0.03
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.24
Consensus pattern (136 bp):
AAAAAAACATGGTCAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGACCAGATCTCCTCA
TCACGTAGGAGCCGCGCCATCCTTAGATAACCAAAATTCCTCATCGCATAGGAACCATGTTTATC
CATTAT
Found at i:6198 original size:136 final size:135
Alignment explanation
Indices: 5815--6198 Score: 450
Period size: 137 Copynumber: 2.8 Consensus size: 135
5805 TGGTCAGATG
** * *
5815 TCCTCATCACGATTGAACAATGTCATCCACCGTCCAGATCTCCTCATCACATAGGAGCC-GCGTC
1 TCCTCATCACGAAGGAACAATGTCATCCACCGACCAGATCTCCTCATCACGTAGGA-CCTGCGTC
* *
5879 ATCCTTATATAACCAAAATTCCTTATCGCATAGGAACCATGTTATCTCCATTATAAAAAAATATG
65 ATCCTTATATAACCAAAATTCCTTATCGCGTAGGAACCATGTTA--TCCATTATAAAAAAACATG
* *
5944 GTCAGACG
128 GACAGACA
* ** * * * *
5952 TCCTCATCACGAAGGAACAGTGGAATCTACCGACTAGATCTCCTCATCACGTAGGA-GTCGCGCC
1 TCCTCATCACGAAGGAACAATGTCATCCACCGACCAGATCTCCTCATCACGTAGGACCT-GCGTC
* *
6016 ATCCTTAGATAACCAAAATTCCTCATCGCGTAGGAACCATGTTTATCCATTATAAAAAAACATGG
65 ATCCTTATATAACCAAAATTCCTTATCGCGTAGGAACCATG-TTATCCATTATAAAAAAACATGG
*
6081 ACATACA
129 ACAGACA
* ** *
6088 TCCTCATCATGAAGGAACAATGTCATCCACTAACCAGATCTCCTCATCACGTAGGACCTACGTCA
1 TCCTCATCACGAAGGAACAATGTCATCCACCGACCAGATCTCCTCATCACGTAGGACCTGCGTCA
* * * *
6153 TCCTTATATAGA-CAGACTTCCCTTATTGCGTAAGAACCATGTTATC
66 TCCTTATATA-ACCAAAATT-CCTTATCGCGTAGGAACCATGTTATC
6199 TCTATTATCC
Statistics
Matches: 206, Mismatches: 35, Indels: 13
0.81 0.14 0.05
Matches are distributed among these distances:
136 94 0.46
137 109 0.53
138 3 0.01
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.26
Consensus pattern (135 bp):
TCCTCATCACGAAGGAACAATGTCATCCACCGACCAGATCTCCTCATCACGTAGGACCTGCGTCA
TCCTTATATAACCAAAATTCCTTATCGCGTAGGAACCATGTTATCCATTATAAAAAAACATGGAC
AGACA
Found at i:6610 original size:73 final size:73
Alignment explanation
Indices: 6226--6629 Score: 499
Period size: 73 Copynumber: 5.5 Consensus size: 73
6216 GAGGGATATC
* ** * *
6226 CAAATCAATTTCGAGTTTGATCTCCGTAGAAGAGTAGTGGATCAGATTCAATCTTCACAGAAGAG
1 CAAATCAATTTCGAGTCTGATCTCCACAGAAGAGTAGTGGAACAGATTCAACCTTCACAGAAGAG
6291 TAGTGAAG
66 TAGTGAAG
* * * * * * *
6299 CAAATCAGA--TCAAGTTTGATCACCACAGAAGAGTAGTGTAACAGATTTAACCTTCACGGAATA
1 CAAATCA-ATTTCGAGTCTGATCTCCACAGAAGAGTAGTGGAACAGATTCAACCTTCACAGAAGA
6362 GTAGTGAAG
65 GTAGTGAAG
* * * * * *
6371 CAAATCAATTTTTGAGTTTGATCTCCATAGAAAAGTAGTGGAA-AAATTCAACCTTCACAAAAGA
1 CAAATCAA-TTTCGAGTCTGATCTCCACAGAAGAGTAGTGGAACAGATTCAACCTTCACAGAAGA
*
6435 GTAATGAAG
65 GTAGTGAAG
* * * * * *
6444 CAAATTAATTTCGAGTCTGATCTCTATAGAAGAGTAGTGGAATAGATTCAGCCTTTCACTGAAGA
1 CAAATCAATTTCGAGTCTGATCTCCACAGAAGAGTAGTGGAACAGATTCAACC-TTCACAGAAGA
6509 GTAGTGAAG
65 GTAGTGAAG
* *
6518 CAAATCAATTTCGAGTCTGATCTCCACATAAGAGTAGTGGAACAGATTCATCCTTCACAGAAGAG
1 CAAATCAATTTCGAGTCTGATCTCCACAGAAGAGTAGTGGAACAGATTCAACCTTCACAGAAGAG
6583 TAGTGAAG
66 TAGTGAAG
* *
6591 CAAATCAATTTCGACTCTGATCTTCACAGAAGAGTAGTG
1 CAAATCAATTTCGAGTCTGATCTCCACAGAAGAGTAGTG
6630 AAGCAAATCA
Statistics
Matches: 283, Mismatches: 42, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
71 1 0.00
72 90 0.32
73 101 0.36
74 91 0.32
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.27
Consensus pattern (73 bp):
CAAATCAATTTCGAGTCTGATCTCCACAGAAGAGTAGTGGAACAGATTCAACCTTCACAGAAGAG
TAGTGAAG
Found at i:6670 original size:41 final size:41
Alignment explanation
Indices: 6570--6654 Score: 127
Period size: 42 Copynumber: 2.0 Consensus size: 41
6560 CAGATTCATC
*
6570 CTTCACAGAAGAGTAGTGAAGCAAATCAATTTCGACTCTGAT
1 CTTCACAGAAGAGTAGTGAAGCAAATCAA-TTCAACTCTGAT
*
6612 CTTCACAGAAGAGTAGTGAAGCAAATCAGA-TCAAGTCTGAT
1 CTTCACAGAAGAGTAGTGAAGCAAATCA-ATTCAACTCTGAT
6653 CT
1 CT
6655 CTATAGAGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
41 11 0.28
42 28 0.70
43 1 0.03
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (41 bp):
CTTCACAGAAGAGTAGTGAAGCAAATCAATTCAACTCTGAT
Found at i:8241 original size:5 final size:6
Alignment explanation
Indices: 8203--8238 Score: 56
Period size: 6 Copynumber: 6.0 Consensus size: 6
8193 TTTTTTGTGT
8203 ATTTTA ATTTTA ATTTTA ATTTTGA ATTTT- ATTTTA
1 ATTTTA ATTTTA ATTTTA ATTTT-A ATTTTA ATTTTA
8239 TTTCCATTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 5 0.18
6 17 0.61
7 6 0.21
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (6 bp):
ATTTTA
Found at i:10332 original size:22 final size:22
Alignment explanation
Indices: 10306--10348 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
10296 TATTATTGAA
10306 TTATTAA-ATATTTAACATATAT
1 TTATTAATATATTTAA-ATATAT
*
10328 TTATTAATATTTTTAAATATA
1 TTATTAATATATTTAAATATA
10349 AAATAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
TTATTAATATATTTAAATATAT
Found at i:10358 original size:30 final size:30
Alignment explanation
Indices: 10289--10359 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 30
10279 TAATTTCATA
*
10289 AAAATAATA-TTATTGAATTATTAAATATTT
1 AAAATAATATTTATTAAATTATTAAATA-TT
* *
10319 AACAT-ATATTTATTAATATTTTTAAATA-T
1 AAAATAATATTTATTAA-ATTATTAAATATT
10348 AAAATAATATTT
1 AAAATAATATTT
10360 TTATTTTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
29 8 0.24
30 16 0.47
31 10 0.29
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (30 bp):
AAAATAATATTTATTAAATTATTAAATATT
Found at i:10412 original size:30 final size:30
Alignment explanation
Indices: 10378--10447 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 30
10368 ATAAGTAATT
* *
10378 AATAAAAT-ATTTAATAATATATATTCTTTC
1 AATAAAATAATATAATAATAT-TATTATTTC
* *
10408 AATAATATAATATAATAATATTATTATTTT
1 AATAAAATAATATAATAATATTATTATTTC
10438 AAT-AAATAAT
1 AATAAAATAAT
10448 TAACATAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
29 6 0.18
30 17 0.50
31 11 0.32
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (30 bp):
AATAAAATAATATAATAATATTATTATTTC
Found at i:10427 original size:31 final size:29
Alignment explanation
Indices: 10389--10447 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
10379 ATAAAATATT
*
10389 TAATAATATATATTCTTTCAATAATATAATA
1 TAATAATAT-TATTATTTCAATAA-ATAATA
*
10420 TAATAATATTATTATTTTAATAAATAAT
1 TAATAATATTATTATTTCAATAAATAAT
10448 TAACATAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 5 0.19
30 12 0.46
31 9 0.35
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.47
Consensus pattern (29 bp):
TAATAATATTATTATTTCAATAAATAATA
Found at i:10965 original size:18 final size:18
Alignment explanation
Indices: 10925--10967 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
10915 TATTTTCAAA
10925 TTAAAATATATAAAAAAT
1 TTAAAATATATAAAAAAT
* * * *
10943 CTAAAATATATGATAATT
1 TTAAAATATATAAAAAAT
10961 TTAAAAT
1 TTAAAAT
10968 TTCAAGGGTG
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (18 bp):
TTAAAATATATAAAAAAT
Found at i:15198 original size:44 final size:44
Alignment explanation
Indices: 15147--15476 Score: 230
Period size: 44 Copynumber: 7.5 Consensus size: 44
15137 AAAAAATCCG
* *
15147 TTCCACTACTCTTTTGTGGAGTTCAGATTTATGATAGAATTTGC
1 TTCCACTACTCTTCTGTGGAGTTCAGATTTATGATAAAATTTGC
* * * *
15191 TTCCACTACTTTTCTGTGGAGTT-TGATACTT-TGCTAAAAAATT-C
1 TTCCACTACTCTTCTGTGGAGTTCAGAT--TTATGAT-AAAATTTGC
* * * **
15235 ATTCCACTACTCTTCCGTGGAGTGCGGATTTATGATTGAATTTGC
1 -TTCCACTACTCTTCTGTGGAGTTCAGATTTATGATAAAATTTGC
* * * *
15280 TTCCACTACTCTTCCGTGGAGTT-TGATCCTT-TGCTGAAAAATT-C
1 TTCCACTACTCTTCTGTGGAGTTCAGAT--TTATGAT-AAAATTTGC
* * ** *
15324 ATTCCACTACTCTTCCGTGGAGATCAGATTTATGATTGAATTTTC
1 -TTCCACTACTCTTCTGTGGAGTTCAGATTTATGATAAAATTTGC
* * * **
15369 TTCCACTACTCTTCTGTGG-TTTGATACTTCGT-TGA-AAAAACTG-
1 TTCCACTACTCTTCTGTGGAGTTCAGA-TT--TATGATAAAATTTGC
* *
15412 TTCCACTACTCTTTTGTGGAGTTCAGATTTATGATTAAATTTGC
1 TTCCACTACTCTTCTGTGGAGTTCAGATTTATGATAAAATTTGC
* *
15456 TTCCAATACTCTTCCGTGGAG
1 TTCCACTACTCTTCTGTGGAG
15477 GCTGAAAATG
Statistics
Matches: 219, Mismatches: 46, Indels: 42
0.71 0.15 0.14
Matches are distributed among these distances:
41 1 0.00
42 3 0.01
43 34 0.16
44 108 0.49
45 66 0.30
46 7 0.03
ACGTcount: A:0.22, C:0.20, G:0.17, T:0.41
Consensus pattern (44 bp):
TTCCACTACTCTTCTGTGGAGTTCAGATTTATGATAAAATTTGC
Found at i:15278 original size:89 final size:89
Alignment explanation
Indices: 15122--15476 Score: 473
Period size: 89 Copynumber: 4.0 Consensus size: 89
15112 TTTCATAAAG
* * * ** *
15122 GTTTCATACTTTGCTAAAAAATCCGTTCCACTACTCTTTTGTGGAGTTCAGATTTATGATAGAAT
1 GTTTGATACTTTGCTAAAAAATTCATTCCACTACTCTTCCGTGGAGTTCAGATTTATGATTGAAT
* *
15187 TTGCTTCCACTACTTTTCTGTGGA
66 TTGCTTCCACTACTCTTCCGTGGA
* *
15211 GTTTGATACTTTGCTAAAAAATTCATTCCACTACTCTTCCGTGGAGTGCGGATTTATGATTGAAT
1 GTTTGATACTTTGCTAAAAAATTCATTCCACTACTCTTCCGTGGAGTTCAGATTTATGATTGAAT
15276 TTGCTTCCACTACTCTTCCGTGGA
66 TTGCTTCCACTACTCTTCCGTGGA
* * *
15300 GTTTGATCCTTTGCTGAAAAATTCATTCCACTACTCTTCCGTGGAGATCAGATTTATGATTGAAT
1 GTTTGATACTTTGCTAAAAAATTCATTCCACTACTCTTCCGTGGAGTTCAGATTTATGATTGAAT
* *
15365 TTTCTTCCACTACTCTTCTGT-G-
66 TTGCTTCCACTACTCTTCCGTGGA
* * * * ** *
15387 GTTTGATACTTCGTTGAAAAAACT-GTTCCACTACTCTTTTGTGGAGTTCAGATTTATGATTAAA
1 GTTTGATACTTTGCT-AAAAAATTCATTCCACTACTCTTCCGTGGAGTTCAGATTTATGATTGAA
*
15451 TTTGCTTCCAATACTCTTCCGTGGA
65 TTTGCTTCCACTACTCTTCCGTGGA
15476 G
1 G
15477 GCTGAAAATG
Statistics
Matches: 233, Mismatches: 30, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
87 66 0.28
88 8 0.03
89 159 0.68
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40
Consensus pattern (89 bp):
GTTTGATACTTTGCTAAAAAATTCATTCCACTACTCTTCCGTGGAGTTCAGATTTATGATTGAAT
TTGCTTCCACTACTCTTCCGTGGA
Found at i:15458 original size:176 final size:178
Alignment explanation
Indices: 15130--15476 Score: 493
Period size: 176 Copynumber: 2.0 Consensus size: 178
15120 AGGTTTCATA
* ** *
15130 CTTTGCTAAAAAATCCGTTCCACTACTCTTTTGTGGAGTTCAGATTTATGATAGAATTTGCTTCC
1 CTTTGCTAAAAAATCCATTCCACTACTCTTCCGTGGAGATCAGATTTATGATAGAATTTGCTTCC
* * *
15195 ACTACTTTTCTGTGGAGTTTGATACTTTGCTAAAAAATTCATTCCACTACTCTTCCGTGGAGTGC
66 ACTACTCTTCTGTGGAGTTTGATACTTCGCTAAAAAACTCATTCCACTACTCTTCCGTGGAGTGC
* * *
15260 GGATTTATGATTGAATTTGCTTCCACTACTCTTCCGTGGAGTTTGATC
131 AGATTTATGATTAAATTTGCTTCCAATACTCTTCCGTGGAGTTTGATC
* * * *
15308 CTTTGCTGAAAAATTCATTCCACTACTCTTCCGTGGAGATCAGATTTATGATTGAATTTTCTTCC
1 CTTTGCTAAAAAATCCATTCCACTACTCTTCCGTGGAGATCAGATTTATGATAGAATTTGCTTCC
* * ** *
15373 ACTACTCTTCTGT-G-GTTTGATACTTCGTTGAAAAAACT-GTTCCACTACTCTTTTGTGGAGTT
66 ACTACTCTTCTGTGGAGTTTGATACTTCGCT-AAAAAACTCATTCCACTACTCTTCCGTGGAGTG
15435 CAGATTTATGATTAAATTTGCTTCCAATACTCTTCCGTGGAG
130 CAGATTTATGATTAAATTTGCTTCCAATACTCTTCCGTGGAG
15477 GCTGAAAATG
Statistics
Matches: 149, Mismatches: 19, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
176 72 0.48
177 8 0.05
178 69 0.46
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40
Consensus pattern (178 bp):
CTTTGCTAAAAAATCCATTCCACTACTCTTCCGTGGAGATCAGATTTATGATAGAATTTGCTTCC
ACTACTCTTCTGTGGAGTTTGATACTTCGCTAAAAAACTCATTCCACTACTCTTCCGTGGAGTGC
AGATTTATGATTAAATTTGCTTCCAATACTCTTCCGTGGAGTTTGATC
Found at i:16191 original size:22 final size:22
Alignment explanation
Indices: 16166--16230 Score: 94
Period size: 22 Copynumber: 2.9 Consensus size: 22
16156 AAAGCTTCCG
16166 TCTTTGAAAAGAGAATCTATCA
1 TCTTTGAAAAGAGAATCTATCA
* *
16188 TCTTTAAAAAGTGAATCTATCA
1 TCTTTGAAAAGAGAATCTATCA
*
16210 TCTTTGAAAAAAGATATCTAT
1 TCTTTGAAAAGAGA-ATCTAT
16231 GTTAAACTCA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
22 31 0.84
23 6 0.16
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.35
Consensus pattern (22 bp):
TCTTTGAAAAGAGAATCTATCA
Found at i:16388 original size:57 final size:56
Alignment explanation
Indices: 16299--16464 Score: 260
Period size: 57 Copynumber: 2.9 Consensus size: 56
16289 GAAACATATT
* *
16299 ACAAGAAGGATTTATCCTAATTCCTATAATGTCTCCACATCTAATCAAATCTCTTC
1 ACAAGAAGGATTTATCCTAATTCCTTTCATGTCTCCACATCTAATCAAATCTCTTC
* *
16355 ACAAGAAGGATTTTATCCTAATTCCTTTCATGTCTCCACATCTAATCATATCTATTC
1 ACAAGAAGGA-TTTATCCTAATTCCTTTCATGTCTCCACATCTAATCAAATCTCTTC
* * *
16412 ACAAAAAGGATTTATCCGAATTCCTTTCATGTCTCCACATCTAATCAGATCTC
1 ACAAGAAGGATTTATCCTAATTCCTTTCATGTCTCCACATCTAATCAAATCTC
16465 GAATAAGGTT
Statistics
Matches: 101, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
56 50 0.50
57 51 0.50
ACGTcount: A:0.32, C:0.25, G:0.08, T:0.35
Consensus pattern (56 bp):
ACAAGAAGGATTTATCCTAATTCCTTTCATGTCTCCACATCTAATCAAATCTCTTC
Found at i:21774 original size:16 final size:16
Alignment explanation
Indices: 21755--21790 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
21745 CAAAAGTTAG
*
21755 AAAAATAA-TAAAATA
1 AAAAATAATTAAAACA
21770 AAAAATAATTAAAACA
1 AAAAATAATTAAAACA
21786 AAAAA
1 AAAAA
21791 ACAAATTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.17
Consensus pattern (16 bp):
AAAAATAATTAAAACA
Found at i:22276 original size:24 final size:24
Alignment explanation
Indices: 22244--22289 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
22234 TAAAATAATT
*
22244 TACTTAATA-TAAATAATTATTAAA
1 TACTGAATACTAAAT-ATTATTAAA
*
22268 TACTGAATACTTAATATTATTA
1 TACTGAATACTAAATATTATTA
22290 GTCCTAGTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 15 0.79
25 4 0.21
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (24 bp):
TACTGAATACTAAATATTATTAAA
Found at i:25034 original size:34 final size:34
Alignment explanation
Indices: 24996--25088 Score: 168
Period size: 34 Copynumber: 2.7 Consensus size: 34
24986 AAGCATCTTG
* *
24996 GGGCCTGAGAGCCTACCCAAGAGAGACTTTACTA
1 GGGCCTAAGAGCCTACCCAAGAGAGAATTTACTA
25030 GGGCCTAAGAGCCTACCCAAGAGAGAATTTACTA
1 GGGCCTAAGAGCCTACCCAAGAGAGAATTTACTA
25064 GGGCCTAAGAGCCTACCCAAGAGAG
1 GGGCCTAAGAGCCTACCCAAGAGAG
25089 TACCTTGGGG
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 57 1.00
ACGTcount: A:0.32, C:0.26, G:0.27, T:0.15
Consensus pattern (34 bp):
GGGCCTAAGAGCCTACCCAAGAGAGAATTTACTA
Found at i:25100 original size:32 final size:32
Alignment explanation
Indices: 24996--25115 Score: 125
Period size: 34 Copynumber: 3.6 Consensus size: 32
24986 AAGCATCTTG
* *
24996 GGGCCTGAGAGCCTACCCAAGAGAGACTTTACTA
1 GGGCCTAAGAGCCTACCCAAGAGAGAC-CTA-TA
**
25030 GGGCCTAAGAGCCTACCCAAGAGAGAATTTACTA
1 GGGCCTAAGAGCCTACCCAAGAGAG-ACCTA-TA
*
25064 GGGCCTAAGAGCCTACCCAAGAGAGTACCT-TG
1 GGGCCTAAGAGCCTACCCAAGAGAG-ACCTATA
* *
25096 GGGCCTTAGAGTCTACCCAA
1 GGGCCTAAGAGCCTACCCAA
25116 AAAAAAAATA
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
32 19 0.25
34 57 0.74
35 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.26, T:0.17
Consensus pattern (32 bp):
GGGCCTAAGAGCCTACCCAAGAGAGACCTATA
Found at i:25134 original size:66 final size:67
Alignment explanation
Indices: 24996--25134 Score: 147
Period size: 66 Copynumber: 2.1 Consensus size: 67
24986 AAGCATCTTG
* * * * * * *
24996 GGGCCTGAGAGCCTACCCAAGAGAGACTTTACTAGGGCCTAAGAGCCTACCCAAGAGAGAATTTA
1 GGGCCTAAGAGCCTACCCAAGAGAGACTCTA-TAGGGCCTAAGAGCCTACCCAAAAAAAAAATAA
25061 CTA
65 CTA
* * *
25064 GGGCCTAAGAGCCTACCCAAGAGAGTAC-CT-TGGGGCCTTAGAGTCTACCCAAAAAAAAAATAA
1 GGGCCTAAGAGCCTACCCAAGAGAG-ACTCTATAGGGCCTAAGAGCCTACCCAAAAAAAAAATAA
*
25127 CTT
65 CTA
25130 GGGCC
1 GGGCC
25135 CTCACAGCAT
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
66 32 0.54
68 25 0.42
69 2 0.03
ACGTcount: A:0.33, C:0.25, G:0.24, T:0.17
Consensus pattern (67 bp):
GGGCCTAAGAGCCTACCCAAGAGAGACTCTATAGGGCCTAAGAGCCTACCCAAAAAAAAAATAAC
TA
Found at i:26281 original size:26 final size:26
Alignment explanation
Indices: 26231--26282 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
26221 CTTGAGGATA
26231 TTTTGGGTCATTTTATACTTCAGGGG
1 TTTTGGGTCATTTTATACTTCAGGGG
* * *
26257 TTTT-GGTTATTTTATAGTTCAAGGG
1 TTTTGGGTCATTTTATACTTCAGGGG
26282 T
1 T
26283 ATTTTAGTCC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.17, C:0.08, G:0.25, T:0.50
Consensus pattern (26 bp):
TTTTGGGTCATTTTATACTTCAGGGG
Found at i:29230 original size:131 final size:131
Alignment explanation
Indices: 29095--29338 Score: 321
Period size: 131 Copynumber: 1.9 Consensus size: 131
29085 TAATTCCAAT
* * * *
29095 TTTTAAAACAAAATAGAAATTTTTATTTATTTCAATTGGGGTAATAAATGAATGTTTTAA-TG-C
1 TTTTAAAACAAAATAGAAATATCTATTTATTTAAATTAGGGTAATAAATGAATGTTTTAATTGAC
* * *
29158 AAGAAAGGTCATTTATTCTCGATTGTAAATCATTAGATATTATCGTTTTCACTTGAATCGATATT
66 -A-AAAGGTCATTTATTCTCGATTGGAAATAATTAAATATTATCGTTTTCACTTGAATCGATATT
29223 GAA
129 GAA
* * * * *
29226 TTTTAAGACGAAATAGTAATATCTCTTTATTTAAATTAGGGTAATAAATGATTGTTTTAATTGAC
1 TTTTAAAACAAAATAGAAATATCTATTTATTTAAATTAGGGTAATAAATGAATGTTTTAATTGAC
* * *
29291 AAAATGTCATTTATTCTCGATTGGAAATAATTAAATGTTATTGTTTTC
66 AAAAGGTCATTTATTCTCGATTGGAAATAATTAAATATTATCGTTTTC
29339 GCTCTTAAAA
Statistics
Matches: 96, Mismatches: 15, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
131 92 0.96
132 3 0.03
133 1 0.01
ACGTcount: A:0.36, C:0.08, G:0.14, T:0.43
Consensus pattern (131 bp):
TTTTAAAACAAAATAGAAATATCTATTTATTTAAATTAGGGTAATAAATGAATGTTTTAATTGAC
AAAAGGTCATTTATTCTCGATTGGAAATAATTAAATATTATCGTTTTCACTTGAATCGATATTGA
A
Found at i:35699 original size:134 final size:134
Alignment explanation
Indices: 35443--37577 Score: 1945
Period size: 134 Copynumber: 16.0 Consensus size: 134
35433 TGTTTAAATG
* * ** * **
35443 TTTC-AGATTTAATATTACCTGAGTAACAACGGAACAAGTCTACCTCGATTCAAT-TTTTCTCGA
1 TTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCT-GA
* * * * * ** *
35506 GTGATAGTGGAATGAATCAACGA-CCCCTGATCTGATCTACCCTCCAGAAGAAGTGGAACATATC
65 GTGACAGTGGAATGAATCAAC-ATCCCCAGATCTGATTTTCCCTCAAGAAGAAGAAGAACAAATC
35570 CATCTC
129 CATCTC
* * * * * * *
35576 TTTCAATAATTGATATTCCCCGAGTAACAGTGGAACAAGTCTGCCTCGATTTAACCTTCCTTAAG
1 TTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTGAG
* * * * *
35641 TGACAGTGGAATGAATCAACATCCCCAGATCTGATATTCCCTCCAGAAGAATAAGAACATATCCC
66 TGACAGTGGAATGAATCAACATCCCCAGATCTGATTTTCCCTCAAGAAGAAGAAGAACAAATCCA
35706 TCTC
131 TCTC
* * * * * * * *
35710 TTCCAAGATTTAATATTCCCTGAGTAACAGTCGAATAAGTCTTCCTCAATTCATTCTTCCCTAAG
1 TTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTGAG
* * * * *
35775 TGACAGTGAAATGGATCAAC-TCCCTTAGATCTGATTTTCCCTCAAGAAGAAGTAGAACAAATCT
66 TGACAGTGGAATGAATCAACATCCC-CAGATCTGATTTTCCCTCAAGAAGAAGAAGAACAAATCC
*
35839 ATCTA
130 ATCTC
* * * * *
35844 TTTCAAGATTTGATATTCCATGAGTGACAGTGGAATAGGTTTGCCTCGATTCAATCTTCCCTGAG
1 TTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTGAG
** * * * *
35909 TGACAGTGGAAT-AGATCAATGTCCCCAAATATGATTTTCCCTCAAGAAGAAGAAAAACAGATCT
66 TGACAGTGGAATGA-ATCAACATCCCCAGATCTGATTTTCCCTCAAGAAGAAGAAGAACAAATC-
*
35973 C-TCAC
129 CATCTC
* * * * * *
35978 TTTCAAGATTTGATATTTCATGAGTAACAGCGTAAGAAGCCTGCCTCGATT-ACATCTTCCCTGA
1 TTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTCGATTCA-ATCTTCCCTGA
* * * * * * * *
36042 GTGACAGTGGAATGAATTAACATCACTAGATATAATTTTCCCTCAAGAATAAG-CGAAACATATA
65 GTGACAGTGGAATGAATCAACATCCCCAGATCTGATTTTCCCTCAAGAAGAAGAAG-AACAAAT-
*
36106 CC-TCTT
128 CCATCTC
* * *
36112 TTTCAAGATTTGATATTCCCT-ACGTGACAGTGGAACAAGTTTGCCTCGATTCAATATTCCCTGA
1 TTTCAAGATTTGATATTCCCTGA-GTAACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTGA
* * * * * * *
36176 GTGAAAGTGGAATGAATCAACATCCCCATATTTAATTTTCCCTCAAGAAAAAG-CGAAACAGATC
65 GTGACAGTGGAATGAATCAACATCCCCAGATCTGATTTTCCCTCAAGAAGAAGAAG-AACAAATC
*
36240 CCTCTC
129 CATCTC
* * * * *
36246 TTTCAAGATTTGATATTCCCAGAGTAACAGTGGAACAATTTTACCTCGATTCAATATTCCCTGAG
1 TTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTGAG
* * *
36311 TGACAATGGCATGAATCAACATCCCCAGATCTGATTTTTCCCTCAAGAAAAAGAAGAACAAATCC
66 TGACAGTGGAATGAATCAACATCCCCAGATCTGA-TTTTCCCTCAAGAAGAAGAAGAACAAATCC
36376 ATCTC
130 ATCTC
* * * * * * * * *
36381 TTTTAAGATTTGATATTCCTTTAATAACAGTGGAACACGTCTGCCTCAATTCAATATTCCTTAAG
1 TTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTGAG
* * * ** * * ** *
36446 TGAAAGTAGAATGGATCAACATCCTTAGATCTGATCTACCCTCCAA-AAGAAGCGGAACATATCC
66 TGACAGTGGAATGAATCAACATCCCCAGATCTGATTTTCCCT-CAAGAAGAAGAAGAACAAATCC
* *
36510 CTCTA
130 ATCTC
* * **
36515 TTTCAAGATATGATATTCCCTGAGTAATAGCAGAACAAGTCTGCCTCGATTCAATCTTCCCTGAG
1 TTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTGAG
* * * * * * ** * *
36580 TGATAATGGAATGGATCAAC-TACCACATATGTGATTTTATCTCAAGAAGAAGCAA-AATAGATC
66 TGACAGTGGAATGAATCAACAT-CCCCAGATCTGATTTTCCCTCAAGAAGAAG-AAGAACAAATC
*
36643 CCTCTC
129 CATCTC
* * *
36649 TTTCAAGATTTGATATTCCCTGAGTGACAGTGGAATAAGTCTGCCTCGATTCAATCTTCCCTAAG
1 TTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTGAG
* * * ** * * *
36714 TAACAGGGGAAT-AGATCAACGTCCTAAGATCTGATTTTCCCTCAAGAAGAAGCATAAAAAATCC
66 TGACAGTGGAATGA-ATCAACATCCCCAGATCTGATTTTCCCTCAAGAAGAAGAAGAACAAATCC
*
36778 ATTTC
130 ATCTC
* *
36783 TTTCAAGATTTGATATT-CCTAGATTAACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCTTGA
1 TTTCAAGATTTGATATTCCCT-GAGTAACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTGA
* * * * * * ** *
36847 GTGATAGTGAAATAAATCAACATCCCTAGATCTAATTTTCCCTCAAGAAAAAGCGGAACAGATCC
65 GTGACAGTGGAATGAATCAACATCCCCAGATCTGATTTTCCCTCAAGAAGAAGAAGAACAAATCC
36912 ATCTC
130 ATCTC
* * * * * * * *
36917 TTTCAATATATGATATTCCCTGAGTAATAGTGGAACAAGTCTACCTCGATTCAATATTTCTTAAG
1 TTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTGAG
* ** ** ** *
36982 TGAAAGTATAATTG-ATCAATGTCCCCAGATCTGATTTTCCCTCTAA-AAGAAGCGGAACATATC
66 TGACAGTGGAA-TGAATCAACATCCCCAGATCTGATTTTCCCTC-AAGAAGAAGAAGAACAAATC
* * *
37045 CCTTTA
129 CATCTC
* * * * * * * *
37051 TTTCAATATTTGATATTCTCTTAGTGATAGTGGAACAAGTCTTCCTCGATTCAATATTCTCTGAG
1 TTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTGAG
* * * * * * *
37116 TGAAAGTAGAATGGATCAAC-TCCCTCATATATGATTTTACCTCAAGAAGAAGCAA-AACAGATC
66 TGACAGTGGAATGAATCAACATCCC-CAGATCTGATTTTCCCTCAAGAAGAAG-AAGAACAAATC
*
37179 CCTCTC
129 CATCTC
*
37185 TTTCAAGATTTGATATTCCCTGAGTTAA-AGCT-GAACAAGTCTGCCTTGATTCAATCTTCCCTG
1 TTTCAAGATTTGATATTCCCTGAG-TAACAG-TGGAACAAGTCTGCCTCGATTCAATCTTCCCTG
* * * * *
37248 AATGACAATGGAAGTG-ATCAACATCCCCATATTTGATTTTCCCTCAAGAAGAA-ATGGAACAAA
64 AGTGACAGTGGAA-TGAATCAACATCCCCAGATCTGATTTTCCCTCAAGAAGAAGA-AGAACAAA
37311 TCCA--T-
127 TCCATCTC
* * *
37316 TTTCAGGATTTGATATTCCCTGAGTGACAGTGGAACAAGTCTGCCTTGATTCAATCTTCCCTGAG
1 TTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTGAG
* * * * * * *
37381 TGAAAGTGGAATAAATCAAC-TCCCCCAGATATGATTTTCCCCCAAGAAAAAGCAGAACAAATCT
66 TGACAGTGGAATGAATCAACAT-CCCCAGATCTGATTTTCCCTCAAGAAGAAGAAGAACAAATCC
*
37445 ATCTA
130 ATCTC
* * * ** *
37450 TTTTAAGATTTGATATTCCCTGAGTGACATTGGAACAAGTCTGAATCGATTCCATCTTCCCTGAG
1 TTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTGAG
* * * * *
37515 TGACAGTGGAATAAATCAAC-TACCCCATATATGATTTTCCCTCAAGTAGAAGAGGAA-AAATCC
66 TGACAGTGGAATGAATCAACAT-CCCCAGATCTGATTTTCCCTCAAGAAGAAGAAGAACAAATCC
37578 CTCATCATAT
Statistics
Matches: 1650, Mismatches: 305, Indels: 94
0.81 0.15 0.05
Matches are distributed among these distances:
130 5 0.00
131 107 0.06
132 2 0.00
133 35 0.02
134 1359 0.82
135 141 0.09
136 1 0.00
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.30
Consensus pattern (134 bp):
TTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTGAG
TGACAGTGGAATGAATCAACATCCCCAGATCTGATTTTCCCTCAAGAAGAAGAAGAACAAATCCA
TCTC
Found at i:38803 original size:17 final size:19
Alignment explanation
Indices: 38781--38822 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
38771 ATAGGGACTG
*
38781 TTTTTATG-AT-TTATACA
1 TTTTTATGCATGTTATAAA
38798 TTTTTATGCATGTTATAAA
1 TTTTTATGCATGTTATAAA
38817 TTTTTA
1 TTTTTA
38823 GGGATATTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.36
18 2 0.09
19 12 0.55
ACGTcount: A:0.29, C:0.05, G:0.07, T:0.60
Consensus pattern (19 bp):
TTTTTATGCATGTTATAAA
Found at i:39891 original size:129 final size:129
Alignment explanation
Indices: 39750--40056 Score: 334
Period size: 130 Copynumber: 2.4 Consensus size: 129
39740 AGGTATGAGG
* * ** * * *
39750 GGTCTTTTATTCTTGATTGAAAATAATT-TGATATTG-TTGTTTTCTCTCGAATTAATACTGATT
1 GGTCATTTATTCTCGATTGAAAATAATTAT-ATA-TGATCATTTTCACTCGAATCAATA-TGA-A
* * * * *
39813 TTTAA-GATGAAATAGTAATTTTTCTTTATTTCAATT-GGTAATAAATGACTATTATAATCCACG
62 TTTAAGGACGAAATAGTAATATCTCTTTATTTCAATTAGGTAATAAATGACTATTATAATACACA
39876 AAA
127 AAA
* * * *
39879 GGTCATTTATTCTCGATTGGAAATCATTATATATGATCATTTTCACTTGAATCGATATGAATTTA
1 GGTCATTTATTCTCGATTGAAAATAATTATATATGATCATTTTCACTCGAATCAATATGAATTTA
* *
39944 AGGACGAAATAGTAATATCTCTTTATTTCAATTAGGGTAATAAATGATTATTTTAATACACAAAA
66 AGGACGAAATAGTAATATCTCTTTATTTCAATTA-GGTAATAAATGACTATTATAATACACAAAA
* * * * *
40009 TGTCATTTATTCTCGATTGAAAATGATTAGATGTTATCATTTTCACTC
1 GGTCATTTATTCTCGATTGAAAATAATTATATATGATCATTTTCACTC
40057 TTAAAATTAT
Statistics
Matches: 148, Mismatches: 25, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
127 5 0.03
128 33 0.22
129 42 0.28
130 68 0.46
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.43
Consensus pattern (129 bp):
GGTCATTTATTCTCGATTGAAAATAATTATATATGATCATTTTCACTCGAATCAATATGAATTTA
AGGACGAAATAGTAATATCTCTTTATTTCAATTAGGTAATAAATGACTATTATAATACACAAAA
Found at i:40022 original size:130 final size:127
Alignment explanation
Indices: 39813--40055 Score: 342
Period size: 130 Copynumber: 1.9 Consensus size: 127
39803 AATACTGATT
* * * * *
39813 TTTAAGATGAAATAGTAATTTTTCTTTATTTCAATTGGTAATAAATGACTATTATAATCCACGAA
1 TTTAAGACGAAATAGTAATATCTCTTTATTTCAATTGGTAATAAATGACTATTATAATACACAAA
* *
39878 AGGTCATTTATTCTCGATTGGAAATCATTATATATGATCATTTTCACTTGAATCGATATGAA
66 AGGTCATTTATTCTCGATTGAAAATCATTAGATATGATCATTTTCACTTGAATCGATATGAA
* *
39940 TTTAAGGACGAAATAGTAATATCTCTTTATTTCAATTAGGGTAATAAATGATTATTTTAATACAC
1 TTTAA-GACGAAATAGTAATATCTCTTTATTTCAATT--GGTAATAAATGACTATTATAATACAC
* * * *
40005 AAAATGTCATTTATTCTCGATTGAAAATGATTAGATGTTATCATTTTCACT
63 AAAAGGTCATTTATTCTCGATTGAAAATCATTAGATATGATCATTTTCACT
40056 CTTAAAATTA
Statistics
Matches: 100, Mismatches: 13, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
127 5 0.05
128 28 0.28
130 67 0.67
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.41
Consensus pattern (127 bp):
TTTAAGACGAAATAGTAATATCTCTTTATTTCAATTGGTAATAAATGACTATTATAATACACAAA
AGGTCATTTATTCTCGATTGAAAATCATTAGATATGATCATTTTCACTTGAATCGATATGAA
Found at i:42150 original size:22 final size:23
Alignment explanation
Indices: 42104--42154 Score: 56
Period size: 21 Copynumber: 2.3 Consensus size: 23
42094 TGAATTATTA
*
42104 AATA-TTT-AAAATATAGTTATC
1 AATATTTTCAAAATATAGATATC
42125 AATAATTTTCAAAATATA-ATAT-
1 AAT-ATTTTCAAAATATAGATATC
42147 AATATTTT
1 AATATTTT
42155 ATTTTAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 8 0.31
22 4 0.15
23 6 0.23
24 8 0.31
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (23 bp):
AATATTTTCAAAATATAGATATC
Found at i:42170 original size:21 final size:21
Alignment explanation
Indices: 42145--42203 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
42135 AAAATATAAT
*
42145 ATAATATTTTATTTTAATATT
1 ATAATATTTTATTTTAATATA
* * *
42166 TTAAT-TTTTAATATTATTATA
1 ATAATATTTT-ATTTTAATATA
*
42187 ATAAGATTTTATTTTAA
1 ATAATATTTTATTTTAA
42204 AAACATATAG
Statistics
Matches: 28, Mismatches: 8, Indels: 4
0.70 0.20 0.10
Matches are distributed among these distances:
20 4 0.14
21 20 0.71
22 4 0.14
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
ATAATATTTTATTTTAATATA
Found at i:42176 original size:15 final size:13
Alignment explanation
Indices: 42146--42203 Score: 62
Period size: 13 Copynumber: 4.2 Consensus size: 13
42136 AAATATAATA
42146 TAATATTTTATTT
1 TAATATTTTATTT
42159 TAATATTTTAATTTT
1 TAATATTTT-A-TTT
**
42174 TAATATTATTATAA
1 TAATATT-TTATTT
*
42188 TAAGATTTTATTT
1 TAATATTTTATTT
42201 TAA
1 TAA
42204 AAACATATAG
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
13 16 0.43
14 8 0.22
15 11 0.30
16 2 0.05
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (13 bp):
TAATATTTTATTT
Found at i:42293 original size:33 final size:35
Alignment explanation
Indices: 42215--42306 Score: 113
Period size: 37 Copynumber: 2.7 Consensus size: 35
42205 AACATATAGA
*
42215 AATATTTTTATTTCAATAATTAATTAATGTAATTTAT
1 AATATTTTTATTTCAATAA--AATTAATGTAATCTAT
42252 AATATTTTTATTTCAATAAAA-TATAT-TAATCT-T
1 AATATTTTTATTTCAATAAAATTA-ATGTAATCTAT
42285 AATATTTTTATTT--ATAAAATTA
1 AATATTTTTATTTCAATAAAATTA
42307 TAGAAATAAT
Statistics
Matches: 52, Mismatches: 1, Indels: 9
0.84 0.02 0.15
Matches are distributed among these distances:
31 6 0.12
32 2 0.04
33 14 0.27
34 7 0.13
35 4 0.08
37 19 0.37
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.53
Consensus pattern (35 bp):
AATATTTTTATTTCAATAAAATTAATGTAATCTAT
Found at i:46237 original size:3 final size:3
Alignment explanation
Indices: 46229--46294 Score: 98
Period size: 3 Copynumber: 22.0 Consensus size: 3
46219 CCAAAGTTTA
*
46229 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ACT A-T ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
46276 ATT AATT ATA ATT ATT ATT
1 ATT -ATT ATT ATT ATT ATT
46295 TTTCTTTTCA
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
2 2 0.03
3 53 0.91
4 3 0.05
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:56314 original size:133 final size:134
Alignment explanation
Indices: 55810--56330 Score: 636
Period size: 133 Copynumber: 3.9 Consensus size: 134
55800 AATCAAACTC
* * *
55810 GATTCAATCTTCCCTAAGTGATAGTGAAATGAATCAACGTCCCCATATATGATTTTCCCTCAAGA
1 GATTCAATCTTCCCTAAGTGATAGTGGAATGAATCAACTTCCCCATATCTGATTTTCCCTCAAGA
* * * *
55875 AGAAGGGGAACAAATCCTTCTCTTTCAAGATTTGATATTCCTTGAGTAACAGTGGAACAAGTCTA
66 AGAAGCGGAACATATCCTTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAACAAGTCTA
*
55940 CCTC
131 CCTA
* *
55944 GATTCAATCTTCCCTAAGTGATAGTGGAATGAATCAACTTCCCCATATCTGATTTTCGCTTAAGA
1 GATTCAATCTTCCCTAAGTGATAGTGGAATGAATCAACTTCCCCATATCTGATTTTCCCTCAAGA
* ** * * * * * * * *
56009 AAAAATGGAACATGT-CTTATCTTTCGAGATATGATATTCCCTGATTGGCAGTAGAACAAGTCTG
66 AGAAGCGGAACATATCCTTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAACAAGTCTA
*
56073 CCCA
131 CCTA
* * * * *
56077 AATTCAATCTTCCCTGACTGATAGTAGAATGAATCAACTTCCCCATATCTGATTTTCTCTCAAGA
1 GATTCAATCTTCCCTAAGTGATAGTGGAATGAATCAACTTCCCCATATCTGATTTTCCCTCAAGA
* *
56142 AGAAGCGGAATC-GATCC-TCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAAGAAGTCT
66 AGAAGCGGAA-CATATCCTTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAACAAGTCT
* *
56205 TCCTT
130 ACCTA
* * * * *
56210 GATTCAATCTTCCCTGAGTGAAAGTGGAATGAATCAACTTCCCCAGATTTGATTTCCCCTCAAGA
1 GATTCAATCTTCCCTAAGTGATAGTGGAATGAATCAACTTCCCCATATCTGATTTTCCCTCAAGA
* * * * *
56275 GGAAGCAGAATATATAC-TCTCTTTCAAGATTTGGTATTCCCTGAGTGACAGTGGAA
66 AGAAGCGGAACATATCCTTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAA
56331 TGAATCAACT
Statistics
Matches: 328, Mismatches: 56, Indels: 7
0.84 0.14 0.02
Matches are distributed among these distances:
133 256 0.78
134 72 0.22
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.31
Consensus pattern (134 bp):
GATTCAATCTTCCCTAAGTGATAGTGGAATGAATCAACTTCCCCATATCTGATTTTCCCTCAAGA
AGAAGCGGAACATATCCTTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAACAAGTCTA
CCTA
Found at i:56321 original size:92 final size:92
Alignment explanation
Indices: 56219--56422 Score: 293
Period size: 92 Copynumber: 2.2 Consensus size: 92
56209 TGATTCAATC
*
56219 TTCCCTGAGTGAAAGTGGAATGAATCAACTTCCCCAGATTTGATTTCCCCTCAAGAGGAAGCAGA
1 TTCCCTGAGTGAAAGTGGAATGAATCAACTTCCCCAGATTTGATTTCCCCTCAAGAAGAAGCAGA
* * *
56284 ATATATACTCTCTTTCAAGATTTG-GTA
66 ACAAATACTCTATTTCAAGATTTGAG-A
* * * * *
56311 TTCCCTGAGTGACAGTGGAATGAATCAACTTCCCTAGATTTGATTTTCCTTCAAGAAGAAGCGGA
1 TTCCCTGAGTGAAAGTGGAATGAATCAACTTCCCCAGATTTGATTTCCCCTCAAGAAGAAGCAGA
*
56376 ACAAATTCTCTATTTCAAGATTTGAGA
66 ACAAATACTCTATTTCAAGATTTGAGA
*
56403 TTCCCTAAGTGAAAGTGGAA
1 TTCCCTGAGTGAAAGTGGAA
56423 CAAGTCTGCC
Statistics
Matches: 99, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
92 98 0.99
93 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.30
Consensus pattern (92 bp):
TTCCCTGAGTGAAAGTGGAATGAATCAACTTCCCCAGATTTGATTTCCCCTCAAGAAGAAGCAGA
ACAAATACTCTATTTCAAGATTTGAGA
Found at i:56398 original size:225 final size:225
Alignment explanation
Indices: 56086--56555 Score: 649
Period size: 225 Copynumber: 2.1 Consensus size: 225
56076 AAATTCAATC
* * * *
56086 TTCCCTGACTGATAGTAGAATGAATCAACTTCCCCATATCTGATTTTCTCTCAAGAAGAAGCGGA
1 TTCCCTGAGTGACAGTGGAATGAATCAACTTCCCCAGATCTGATTTTCTCTCAAGAAGAAGCGGA
* * * * * * * **
56151 ATCGATCCTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAAGAAGTCTTCCTTGATTCA
66 ATCAATCCTCTATTTCAAGATTTGAGATTCCCTAAGTGAAAGTGGAACAAGTCTGCCCCGATTCA
* *
56216 ATCTTCCCTGAGTGA-AAGTGGAATGAATCAACTTCCCCAGATTTGATTTCCCCTCAAGAGGAAG
131 ATCTTCCCTGAGTGATAA-TGGAATGAATAAACTTCCCCAGATTTGATTTCCCCTCAAGAAGAAG
* * *
56280 CAGAATATATACTCTCTTTCAAGATTTGGTA
195 CAGAACATATACTCCCTTTCAAGATTTGATA
* *
56311 TTCCCTGAGTGACAGTGGAATGAATCAACTTCCCTAGATTTGATTTTC-CTTCAAGAAGAAGCGG
1 TTCCCTGAGTGACAGTGGAATGAATCAACTTCCCCAGATCTGATTTTCTC-TCAAGAAGAAGCGG
*
56375 AA-CAAATTCTCTATTTCAAGATTTGAGATTCCCTAAGTGAAAGTGGAACAAGTCTGCCCCGATT
65 AATC-AATCCTCTATTTCAAGATTTGAGATTCCCTAAGTGAAAGTGGAACAAGTCTGCCCCGATT
* * *
56439 CAATCTTCCCTGAGTGATAATGGAATTAATAAACTTCCCCAGATTTTATTTTCCCTCAAGAAGAA
129 CAATCTTCCCTGAGTGATAATGGAATGAATAAACTTCCCCAGATTTGATTTCCCCTCAAGAAGAA
* *
56504 GTAGAACATATCCTCCCTTTCAAGATTTGATA
194 GCAGAACATATACTCCCTTTCAAGATTTGATA
*
56536 TTCCTTGAGTGACAGTGGAA
1 TTCCCTGAGTGACAGTGGAA
56556 AAAGTCTGCC
Statistics
Matches: 215, Mismatches: 27, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
224 2 0.01
225 211 0.98
226 2 0.01
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (225 bp):
TTCCCTGAGTGACAGTGGAATGAATCAACTTCCCCAGATCTGATTTTCTCTCAAGAAGAAGCGGA
ATCAATCCTCTATTTCAAGATTTGAGATTCCCTAAGTGAAAGTGGAACAAGTCTGCCCCGATTCA
ATCTTCCCTGAGTGATAATGGAATGAATAAACTTCCCCAGATTTGATTTCCCCTCAAGAAGAAGC
AGAACATATACTCCCTTTCAAGATTTGATA
Found at i:56448 original size:133 final size:133
Alignment explanation
Indices: 56311--57804 Score: 1557
Period size: 133 Copynumber: 11.2 Consensus size: 133
56301 AGATTTGGTA
* * * *
56311 TTCCCTGAGTGACAGTGGAATGAATCAACTTCCCTAGATTTGATTTTCCTTCAAGAAGAAGCGGA
1 TTCCCTGAGTGATAGTGGAATGAATCAACTTCCCCAGATTTGATTTTCCCTCAAGAAGAAGCAGA
* * * * * * * *
56376 ACAAATTCTCTATTTCAAGATTTGAGATTCCCTAAGTGAAAGTGGAACAAGTCTGCCCCGATTCA
66 ACAGATCCTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAACAAGTCTACCTCGATTCA
56441 ATC
131 ATC
* * * * *
56444 TTCCCTGAGTGATAATGGAATTAATAAACTTCCCCAGATTTTATTTTCCCTCAAGAAGAAGTAGA
1 TTCCCTGAGTGATAGTGGAATGAATCAACTTCCCCAGATTTGATTTTCCCTCAAGAAGAAGCAGA
* * * * *
56509 ACATATCCTCCCTTTCAAGATTTGATATTCCTTGAGTGACAGTGGAAAAAGTCTGCCTCGATTCA
66 ACAGATCCTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAACAAGTCTACCTCGATTCA
56574 ATC
131 ATC
* * * * * *
56577 TTCCTTGAGTGACAGTAGG-ATGAATCAACTTCCCCAGATCTGATTTTCCCTTAATAAGAAGTAG
1 TTCCCTGAGTGATAGT-GGAATGAATCAACTTCCCCAGATTTGATTTTCCCTCAAGAAGAAGCAG
* * * * * * *
56641 AACA-AACCATCTCTTTCAAGATTTGATATTTCCTAAGTGATAGTGGAACATGTCTTCCTTGATT
65 AACAGATCC-TCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAACAAGTCTACCTCGATT
56705 CAATC
129 CAATC
* * * * * * * * * *
56710 TTCCCTGAGTGATACTGGAATGAATCAACTTCTCTAGATCTGATTTTTCTTTAAAAAAAAGCACA
1 TTCCCTGAGTGATAGTGGAATGAATCAACTTCCCCAGATTTGATTTTCCCTCAAGAAGAAGCAGA
* * * * * * *
56775 AGAGATCCATCTATTTCAAGATTTGATATTCCCTTAGTGATAATGGAACAAGTCTACATCAATTC
66 ACAGATCC-TCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAACAAGTCTACCTCGATTC
56840 AATC
130 AATC
* * * ** * * * **
56844 TTCCCTAATTGACAGTGGAATGGTTCAA-TGTCCCTAGATCTAATTTTCCCTCAAGAAGAAGTGG
1 TTCCCTGAGTGATAGTGGAATGAATCAACT-TCCCCAGATTTGATTTTCCCTCAAGAAGAAGCAG
* * * * * *
56908 AACATATCCTATCTTTCAAGATTTGATATTCCCTGAGTGACAGTTGAATAACTCTACCCCGATTC
65 AACAGATCCTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAACAAGTCTACCTCGATTC
56973 AATC
130 AATC
* ** * * * *
56977 TT-CCTGAGTGATAGT-GAATTGAATCAACATCCTAATATATGATTTTTCCTCAAGAAGAAGTAG
1 TTCCCTGAGTGATAGTGGAA-TGAATCAACTTCCCCAGATTTGATTTTCCCTCAAGAAGAAGCAG
* * * * * * * * * *
57040 AACAGATCCCTCTTTTTCAATATTTAATATTCACTAAGTGACAGCGGAACAAGTTTTCCACTATT
65 AACAGAT-CCTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAACAAGTCTACCTCGATT
57105 CAATC
129 CAATC
** * * * * * *
57110 TTCTTTGAGCGACAGTGGAATGAATC-AGTTTCCCATATTTGATTTTCCCTCAAGAAGAAGCACA
1 TTCCCTGAGTGATAGTGGAATGAATCAACTTCCCCAGATTTGATTTTCCCTCAAGAAGAAGCAGA
* * * * * * *
57174 ACATATCGTCTCTTTCAAAATTTGATATTCCATGAGTGACTGTGGAACAAGTCTGCCTCGATTTA
66 ACAGATCCTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAACAAGTCTACCTCGATTCA
*
57239 ATA
131 ATC
* * * *
57242 TTCCCTGAGTGACAGTGGAATGAATAAACTTCCCCATATTTGATTTTTCCCTCAAGAAGAAGCGG
1 TTCCCTGAGTGATAGTGGAATGAATCAACTTCCCCAGATTTGA-TTTTCCCTCAAGAAGAAGCAG
* * *
57307 AACAGATCCTCTTTTTCAAGATTTAATATTCCCTCAGTG-CTAGTGGAACAAGTCTACACT-GAT
65 AACAGATCCTCTCTTTCAAGATTTGATATTCCCTGAGTGAC-AGTGGAACAAGTCTAC-CTCGAT
57370 TCAATC
128 TCAATC
* * * * *
57376 TTCCCTGAGTGATAGTAGAATGAATCAACTTCCCCATATCTAATTTTCTCTCAAGAAGAAGCAGA
1 TTCCCTGAGTGATAGTGGAATGAATCAACTTCCCCAGATTTGATTTTCCCTCAAGAAGAAGCAGA
** * * * *
57441 ATTGATCATCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAAGAAGTCTTCCTCGATTAA
66 ACAGATCCTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAACAAGTCTACCTCGATTCA
57506 ATC
131 ATC
* * * *
57509 TTCCCTGAGTGATAGTGGAATGAATCAACTTCCCCAGATATGATTTTCCCTCAAGAGGAAGAAAA
1 TTCCCTGAGTGATAGTGGAATGAATCAACTTCCCCAGATTTGATTTTCCCTCAAGAAGAAGCAGA
* * * * * *
57574 ATAGATACTCTCTTTCAAGATTTGGTATTCCCTGAGTGACAGTGAAACAAGTCTGCCCCGATTCA
66 ACAGATCCTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAACAAGTCTACCTCGATTCA
57639 ATC
131 ATC
* * * * *
57642 TTCCCCGAGTGATAGTGGATTGAATCAACATTCCTCAGATATGATTTTCCCTCAAGAAGAAGTAG
1 TTCCCTGAGTGATAGTGGAATGAATCAAC-TTCCCCAGATTTGATTTTCCCTCAAGAAGAAGCAG
* * * *
57707 AACATATCCATCTCTTTCAAGATTTGATATTCCCTGAGTGGCAGTGAAACAAGTCTACCTTGATT
65 AACAGATCC-TCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAACAAGTCTACCTCGATT
57772 CAATC
129 CAATC
* *
57777 TTCCCTGAAG-AATAGTTGAATGAATCAA
1 TTCCCTG-AGTGATAGTGGAATGAATCAA
57805 TGTTTCTCGA
Statistics
Matches: 1126, Mismatches: 216, Indels: 36
0.82 0.16 0.03
Matches are distributed among these distances:
131 3 0.00
132 125 0.11
133 642 0.57
134 273 0.24
135 81 0.07
136 2 0.00
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (133 bp):
TTCCCTGAGTGATAGTGGAATGAATCAACTTCCCCAGATTTGATTTTCCCTCAAGAAGAAGCAGA
ACAGATCCTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAACAAGTCTACCTCGATTCA
ATC
Found at i:56656 original size:358 final size:357
Alignment explanation
Indices: 55953--56688 Score: 928
Period size: 358 Copynumber: 2.1 Consensus size: 357
55943 CGATTCAATC
* *
55953 TTCCCTAAGTGATAGTGGAATGAATCAACTTCCCCATATCTGATTTTCGCTTAAGAAAAAATGGA
1 TTCCCTAAGTGATAGTGGAATGAATCAACTTCCCCAGATCTGATTTTCGCTTAAGAAAAAACGGA
* * * * **
56018 ACATGTCTTATCTTTCGAGATATGATATTCCCTGATTGGCAGTAGAACAAGTCTGCCCAAATTCA
66 ACATGTCTTA-CTTTCAAGATATGAGATTCCCTAAGTGAAAGTAGAACAAGTCTGCCCAAATTCA
* * * *
56083 ATCTTCCCTGACTGATAGTAGAATGAATCAACTTCCCCATATCTGATTTTCTCTCAAGAAGAAGC
130 ATCTTCCCTGACTGATAATAGAATGAATAAACTTCCCCAGATCTGATTTTCCCTCAAGAAGAAGC
* * * * *
56148 GGAATCGATCCTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAAGAAGTCTTCCTTGAT
195 AGAATCGATCCTCCCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAAAAAGTCTGCCTCGAT
* *
56213 TCAATCTTCCCTGAGTGAAAGTGGAATGAATCAACTTCCCCAGATTTGATTTCCCCTCAAGAGGA
260 TCAATCTTCCCTGAGTGAAAGTGGAATGAATCAACTTCCCCAGATCTGATTTCCCCTCAAGAAGA
* *
56278 AGCAGAATATATACTCTCTTTCAAGATTTGGTA
325 AGCAGAACATATACTCTCTTTCAAGATTTGATA
* * * * * *
56311 TTCCCTGAGTGACAGTGGAATGAATCAACTTCCCTAGATTTGATTTTC-CTTCAAGAAGAAGCGG
1 TTCCCTAAGTGATAGTGGAATGAATCAACTTCCCCAGATCTGATTTTCGCTT-AAGAAAAAACGG
* * **
56375 AACAAAT-TCTCTA-TTTCAAGATTTGAGATTCCCTAAGTGAAAGTGGAACAAGTCTGCCCCGAT
65 AAC--ATGTCT-TACTTTCAAGATATGAGATTCCCTAAGTGAAAGTAGAACAAGTCTGCCCAAAT
* * * * *
56438 TCAATCTTCCCTGAGTGATAATGGAATTAATAAACTTCCCCAGATTTTATTTTCCCTCAAGAAGA
127 TCAATCTTCCCTGACTGATAATAGAATGAATAAACTTCCCCAGATCTGATTTTCCCTCAAGAAGA
* * *
56503 AGTAGAA-CATATCCTCCCTTTCAAGATTTGATATTCCTTGAGTGACAGTGGAAAAAGTCTGCCT
192 AGCAGAATC-GATCCTCCCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAAAAAGTCTGCCT
* * * *
56567 CGATTCAATCTTCCTTGAGTGACAGTAGG-ATGAATCAACTTCCCCAGATCTGATTTTCCCTTAA
256 CGATTCAATCTTCCCTGAGTGAAAGT-GGAATGAATCAACTTCCCCAGATCTGATTTCCCCTCAA
* *
56631 TAAGAAGTAGAACA-A-ACCATCTCTTTCAAGATTTGATA
320 GAAGAAGCAGAACATATA-C-TCTCTTTCAAGATTTGATA
*
56669 TTTCCTAAGTGATAGTGGAA
1 TTCCCTAAGTGATAGTGGAA
56689 CATGTCTTCC
Statistics
Matches: 322, Mismatches: 48, Indels: 16
0.83 0.12 0.04
Matches are distributed among these distances:
356 1 0.00
357 6 0.02
358 306 0.95
359 5 0.02
360 4 0.01
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (357 bp):
TTCCCTAAGTGATAGTGGAATGAATCAACTTCCCCAGATCTGATTTTCGCTTAAGAAAAAACGGA
ACATGTCTTACTTTCAAGATATGAGATTCCCTAAGTGAAAGTAGAACAAGTCTGCCCAAATTCAA
TCTTCCCTGACTGATAATAGAATGAATAAACTTCCCCAGATCTGATTTTCCCTCAAGAAGAAGCA
GAATCGATCCTCCCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAAAAAGTCTGCCTCGATT
CAATCTTCCCTGAGTGAAAGTGGAATGAATCAACTTCCCCAGATCTGATTTCCCCTCAAGAAGAA
GCAGAACATATACTCTCTTTCAAGATTTGATA
Found at i:56926 original size:400 final size:397
Alignment explanation
Indices: 56311--57804 Score: 1633
Period size: 400 Copynumber: 3.7 Consensus size: 397
56301 AGATTTGGTA
* * **
56311 TTCCCTGAGTGACAGTGGAATGAATCAACTTCCCTAGATTTGATTTTCCTTCAAGAAGAAGCGGA
1 TTCCCTGAGTGACAGTGGAATGAATCAACTTCCCCAGATTTGATTTTCCCTCAAGAAGAAGCACA
* * *
56376 ACAAATTCTCTATTTCAAGATTTGAGATTCCCTAAGTGA-AAGTGGAACAAGTCTGCCCCGATTC
66 ACAGA-TCTCTATTTCAAGATTTGATATTCCCTGAGTGATAA-TGGAACAAGTCTGCCCCGATTC
* * * *
56440 AATCTTCCCTGAGTGATAATGGAATTAATAAACTTCCCCAGATTTTATTTTCCCTCAAGAAGAAG
129 AATCTTCCCTGAGTGACAGTGGAATGAATAAACTTCCCCAGATTTAATTTTCCCTCAAGAAGAAG
* * *
56505 TAGAACATATCCTCCCTTTCAAGATTTGATATTCCTTGAGTGACAGTGGAAAAAGTCTGCCTCGA
194 TAGAACATATCCTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAAAAAGTCTACCTCGA
* * * * *
56570 TTCAATCTTCCTTGAGTGACAGTAGGATGAATCAACTTCCCCAGATCTGATTTTCCCTTAATAAG
259 TTCAATCTTCC-TGAGTGATAGTAGAATGAATCAACTTCCCCATATCTGATTTTCCCTCAAGAAG
* *
56635 AAGTAGAACAAACCATCTCTTTCAAGATTTGATATTTCCTAAGTGATAGTGGAACATGTCTTCCT
323 AAGTAGAACAAACCATCTCTTTCAAGATTTGATATTTCCTAAGTGACAGTGGAACAAGTCTTCCT
56700 TGATTCAATC
388 TGATTCAATC
* * * * * * * * * *
56710 TTCCCTGAGTGATACTGGAATGAATCAACTTCTCTAGATCTGATTTTTCTTTAAAAAAAAGCACA
1 TTCCCTGAGTGACAGTGGAATGAATCAACTTCCCCAGATTTGATTTTCCCTCAAGAAGAAGCACA
* * * ** *
56775 AGAGATCCATCTATTTCAAGATTTGATATTCCCTTAGTGATAATGGAACAAGTCTACATCAATTC
66 ACAGAT-C-TCTATTTCAAGATTTGATATTCCCTGAGTGATAATGGAACAAGTCTGCCCCGATTC
* * ** * * *
56840 AATCTTCCCTAATTGACAGTGGAATGGTTCAA-TGTCCCTAGATCTAATTTTCCCTCAAGAAGAA
129 AATCTTCCCTGAGTGACAGTGGAATGAATAAACT-TCCCCAGATTTAATTTTCCCTCAAGAAGAA
* * * * * *
56904 GTGGAACATATCCTATCTTTCAAGATTTGATATTCCCTGAGTGACAGTTGAATAACTCTACCCCG
193 GTAGAACATATCCTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAAAAAGTCTACCTCG
* ** * *
56969 ATTCAATCTTCCTGAGTGATAGT-GAATTGAATCAACATCCTAATATATGATTTTTCCTCAAGAA
258 ATTCAATCTTCCTGAGTGATAGTAGAA-TGAATCAACTTCCCCATATCTGATTTTCCCTCAAGAA
* * * * * * *
57033 GAAGTAGAACAGATCCCTCTTTTTCAATATTTAATA-TTCACTAAGTGACAGCGGAACAAGTTTT
322 GAAGTAGAACA-AACCATCTCTTTCAAGATTTGATATTTC-CTAAGTGACAGTGGAACAAGTCTT
*
57097 CCACT-ATTCAATC
385 CC-TTGATTCAATC
** * * * *
57110 TTCTTTGAGCGACAGTGGAATGAATC-AGTTTCCCATATTTGATTTTCCCTCAAGAAGAAGCACA
1 TTCCCTGAGTGACAGTGGAATGAATCAACTTCCCCAGATTTGATTTTCCCTCAAGAAGAAGCACA
* * * * * * *
57174 ACATATCGTCTCTTTCAAAATTTGATATTCCATGAGTGACT-GTGGAACAAGTCTGCCTCGATTT
66 ACAGATC-TCTATTTCAAGATTTGATATTCCCTGAGTGA-TAATGGAACAAGTCTGCCCCGATTC
* * *
57238 AATATTCCCTGAGTGACAGTGGAATGAATAAACTTCCCCATATTTGATTTTTCCCTCAAGAAGAA
129 AATCTTCCCTGAGTGACAGTGGAATGAATAAACTTCCCCAGATTT-AATTTTCCCTCAAGAAGAA
** * * * * *
57303 GCGGAACAGATCCTCTTTTTCAAGATTTAATATTCCCTCAGTG-CTAGTGGAACAAGTCTACACT
193 GTAGAACATATCCTCTCTTTCAAGATTTGATATTCCCTGAGTGAC-AGTGGAAAAAGTCTAC-CT
* *
57367 -GATTCAATCTTCCCTGAGTGATAGTAGAATGAATCAACTTCCCCATATCTAATTTTCTCTCAAG
256 CGATTCAATCTT-CCTGAGTGATAGTAGAATGAATCAACTTCCCCATATCTGATTTTCCCTCAAG
* *** * * * *
57431 AAGAAGCAGAATTGATCATCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAAGAAGTCTT
320 AAGAAGTAGAACAAACCATCTCTTTCAAGATTTGATATTTCCTAAGTGACAGTGGAACAAGTCTT
* *
57496 CCTCGATTAAATC
385 CCTTGATTCAATC
* * * * *
57509 TTCCCTGAGTGATAGTGGAATGAATCAACTTCCCCAGATATGATTTTCCCTCAAGAGGAAGAAAA
1 TTCCCTGAGTGACAGTGGAATGAATCAACTTCCCCAGATTTGATTTTCCCTCAAGAAGAAGCACA
* * * * * *
57574 ATAGATACTCTCTTTCAAGATTTGGTATTCCCTGAGTGACAGTGAAACAAGTCTGCCCCGATTCA
66 ACAGAT-CTCTATTTCAAGATTTGATATTCCCTGAGTGATAATGGAACAAGTCTGCCCCGATTCA
* * * * * * *
57639 ATCTTCCCCGAGTGATAGTGGATTGAATCAACATTCCTCAGATATGATTTTCCCTCAAGAAGAAG
130 ATCTTCCCTGAGTGACAGTGGAATGAATAAAC-TTCCCCAGATTTAATTTTCCCTCAAGAAGAAG
* *
57704 TAGAACATATCCATCTCTTTCAAGATTTGATATTCCCTGAGTGGCAGT-GAAACAAGTCTACCTT
194 TAGAACATATCC-TCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAAA-AAGTCTACCTC
* *
57768 GATTCAATCTTCCCTGAAG-AATAGTTGAATGAATCAA
257 GATTCAATCTT-CCTG-AGTGATAGTAGAATGAATCAA
57805 TGTTTCTCGA
Statistics
Matches: 899, Mismatches: 170, Indels: 50
0.80 0.15 0.04
Matches are distributed among these distances:
398 84 0.09
399 293 0.33
400 433 0.48
401 86 0.10
402 3 0.00
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (397 bp):
TTCCCTGAGTGACAGTGGAATGAATCAACTTCCCCAGATTTGATTTTCCCTCAAGAAGAAGCACA
ACAGATCTCTATTTCAAGATTTGATATTCCCTGAGTGATAATGGAACAAGTCTGCCCCGATTCAA
TCTTCCCTGAGTGACAGTGGAATGAATAAACTTCCCCAGATTTAATTTTCCCTCAAGAAGAAGTA
GAACATATCCTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAAAAAGTCTACCTCGATT
CAATCTTCCTGAGTGATAGTAGAATGAATCAACTTCCCCATATCTGATTTTCCCTCAAGAAGAAG
TAGAACAAACCATCTCTTTCAAGATTTGATATTTCCTAAGTGACAGTGGAACAAGTCTTCCTTGA
TTCAATC
Found at i:71877 original size:35 final size:38
Alignment explanation
Indices: 71831--71911 Score: 114
Period size: 38 Copynumber: 2.2 Consensus size: 38
71821 TTTGAGAATT
* *
71831 TGGTGATGATAT-GGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCCGTGATAATGGAAGATGGACTA
*
71866 TGGTGATGATATAGGCCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCCGTGATAATGGAAGATGGACTA
71904 TGGTGATG
1 TGGTGATG
71912 GAAATAGTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
35 12 0.30
36 8 0.20
37 4 0.10
38 16 0.40
ACGTcount: A:0.26, C:0.05, G:0.38, T:0.31
Consensus pattern (38 bp):
TGGTGATGATATAGGCCGTGATAATGGAAGATGGACTA
Done.